The general transcription factor, TFIID, consists of the TATA binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. One of the TAFs, TAFII250, has acetyl transferase (AT) activity that is necessary for transcription of MHC class I genes: inhibition of the AT activity represses transcription. To identify potential cellular factors that might regulate the AT activity of TAFII250, a yeast two-hybrid library was screened with a TAFII250 segment (848-1279 aa) that spanned part of its AT domain and its RAP74 binding domain. The TFIID component, TAFII55, was isolated and found to interact predominantly with the RAP74-binding domain. TAFII55 binding to TAFII250 inhibits its AT activity. Importantly, addition of recombinant TAFII55 to in vitro transcription assays inhibits TAFII250-dependent MHC class I transcription. Thus, TAFII55 is capable of regulating TAFII250 function by modulating its AT activity. The biological role of TAFII55-repression of TAFII250 is being investigated by studying transcription of in vitro assembled pre-initiation complexes (PIC), in which it can be shown that TAFII55 assembles with the PIC.